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- PDB-5gxb: crystal structure of a LacY/Nanobody complex -

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Basic information

Entry
Database: PDB / ID: 5gxb
Titlecrystal structure of a LacY/Nanobody complex
Components
  • Lactose permease
  • nanobody
KeywordsTRANSPORT PROTEIN / transporter
Function / homology
Function and homology information


lactose:proton symporter activity / lactose transport / cytidine transmembrane transporter activity / carbohydrate:proton symporter activity / uridine transmembrane transporter activity / lactose binding / : / carbohydrate transport / membrane / plasma membrane
Similarity search - Function
LacY/RafB permease family / LacY/RafB permease family, conserved site / LacY proton/sugar symporter / LacY family proton/sugar symporters signature 1. / LacY family proton/sugar symporters signature 2. / MFS general substrate transporter like domains / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; / MFS transporter superfamily ...LacY/RafB permease family / LacY/RafB permease family, conserved site / LacY proton/sugar symporter / LacY family proton/sugar symporters signature 1. / LacY family proton/sugar symporters signature 2. / MFS general substrate transporter like domains / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; / MFS transporter superfamily / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsJiang, X. / Wu, J.P. / Yan, N. / Kaback, H.R.
Funding support United States, China, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1547801 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM120043 United States
Ministry of Science and Technology (MoST, China)2011CB910501 China
National Natural Science Foundation of China (NSFC)31125009 and 91017011 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Crystal structure of a LacY-nanobody complex in a periplasmic-open conformation.
Authors: Jiang, X. / Smirnova, I. / Kasho, V. / Wu, J. / Hirata, K. / Ke, M. / Pardon, E. / Steyaert, J. / Yan, N. / Kaback, H.R.
History
DepositionSep 16, 2016Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 12, 2022Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.deposit_site
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactose permease
B: nanobody


Theoretical massNumber of molelcules
Total (without water)63,3082
Polymers63,3082
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-9 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.543, 96.543, 145.025
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Lactose permease / Lactose-proton symport


Mass: 47618.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lacY, b0343, JW0334 / Production host: Escherichia coli (E. coli) / References: UniProt: P02920
#2: Antibody nanobody


Mass: 15690.347 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 100mM MES pH 6.0, 100mM (NH4)2C4H4O6, 43% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→48.342 Å / Num. obs: 10364 / % possible obs: 97.1 % / Redundancy: 29.2 % / CC1/2: 0.988 / Net I/σ(I): 7.9
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 15.3 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.485 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2405: ???)refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementResolution: 3.3→48.342 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3465 513 4.95 %
Rwork0.3397 --
obs0.34 10364 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→48.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4121 0 0 0 4121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154242
X-RAY DIFFRACTIONf_angle_d1.8445747
X-RAY DIFFRACTIONf_dihedral_angle_d19.9971442
X-RAY DIFFRACTIONf_chiral_restr0.117631
X-RAY DIFFRACTIONf_plane_restr0.007708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.6320.38521280.39512221X-RAY DIFFRACTION89
3.632-4.15730.36231190.36262483X-RAY DIFFRACTION98
4.1573-5.23680.34291190.332529X-RAY DIFFRACTION98
5.2368-48.34680.32881470.32012618X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -19.0104 Å / Origin y: -19.8168 Å / Origin z: 36.5466 Å
111213212223313233
T0.6512 Å2-0.0091 Å20.0474 Å2-0.6581 Å2-0.0345 Å2--0.7028 Å2
L0.8694 °2-0.6179 °20.2841 °2-0.6132 °2-0.1749 °2--1.1048 °2
S-0.0247 Å °-0.0854 Å °-0.1407 Å °0.0341 Å °0.1813 Å °0.0485 Å °-0.1055 Å °-0.0494 Å °-0.1399 Å °
Refinement TLS groupSelection details: all

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